sigminer (version 1.0.6)

sig_convert: Convert Signatures between different Genomic Distribution of Components

Description

Converts signatures between two representations relative to different sets of mutational opportunities. Currently, only SBS signature is supported.

Usage

sig_convert(sig, from = "human-genome", to = "human-exome")

Arguments

sig

a Signature object obtained either from sig_extract or sig_auto_extract, or just a raw signature matrix with row representing components (motifs) and column representing signatures.

from

either one of "human-genome" and "human-exome" or an opportunity matrix (repeated n columns with each row represents the total number of mutations for a component, n is the number of signature).

to

same as from.

Value

a matrix.

Details

The default opportunity matrix for "human-genome" and "human-exome" comes from COSMIC signature database v2 and v3.

References

convert_signatures function from sigfit package.

Examples

# NOT RUN {
# Load SBS signature
load(system.file("extdata", "toy_mutational_signature.RData",
  package = "sigminer", mustWork = TRUE
))
# Exome-relative to Genome-relative
sig_converted <- sig_convert(sig2,
  from = "human-exome",
  to = "human-genome"
)
sig_converted

show_sig_profile(sig2, style = "cosmic")
show_sig_profile(sig_converted, style = "cosmic")
# }